Trained to Kill
by cg's-gal-72689
Summary: Sydney went to Wittenberg to find out the truth. What she found there, though, was that her training as a child had a permanent effect. But she also has to work with someone new. Jason Bourne. Bourne IdentityAlias Crossover. More details inside.
1. Prologue

Trained to Kill  
  
Sydney went to Wittenberg to find out the truth. What she found there, though, was that her training as a child had a permanent effect. She forgot two years for a reason. Now, she must work with someone she loves. But she also has to work with someone new. His name is Jason Bourne. S/V romance. PG-13 for some language.  
  
AN: This is set after the season 3 finale, so any spoilers for that are fair game. Yes, this is a Bourne Identity/Supremacy and Alias crossover. I thought it up while having a goofy conversation with a fellow Alias fan. There will be spoilers for both movies in here as well. I'm not actually sure where I'm going to go with this, but I have an instinct about this (Ah, Alias quotes). So please R&R!  
  
Prologue

Treadstone. Sounds like a kind of tire, doesn't it? There's Bridgestone and Firestone. You'd think it was a tire. But, no. It's a secret branch of the CIA that is now just a distant memory. Or so they would want you to think. The truth is out there. I am supposed to be the last Treadstone agent. I'm supposed to be the only one who has to live through this hell. Why? Because I've killed the rest of them. Except there are more. They were made this way by another "project" of the CIA. One I just found out I was enlisted in as a child. One over a hundred kids were subjected to. Another project that sounds like something else. Project Christmas.  
I am David Webb. Or I was. Now I am Jason Bourne. I am a next generation weapon. A deadly one. I went back home to find my past. And I found it all right. My family has been dead for years. They died in a car crash. But they still had a house. Apparently it didn't get sold because, before I lost my memory, I lived there in between some missions.  
I learned everything at that house. I found a letter framed in my old room. It was from when I was about six. I was asked to participate in an achievement program for the gifted. On my desk were papers covered in drawings. They were very sloppy, but I had drawn a tower. But as I looked, I saw lines drawn. It was a puzzle. I had written two words next to it. "Project: Christmas" Another drawing had a disassembled gun. It, too, had "Project: Christmas" written next to it. That night I began to have flashbacks. I was putting a gun together, and putting the pieces of the tower on top of each other. It was training. I was trained as a child to be a spy. And though I'm sure there was an extensive amount of brainwashing, the memories were coming back.  
I used any resources I could, legal or otherwise, to find out about this project. After hacking into a few databases I found the info I needed. The project had been created in Los Angeles. So that's where I'm headed now. To L.A. to find whoever made this. I know there are others. There could be other kids in danger. There could be sleeper agents out there. And there are answers out there. I'm going to find them.


	2. The Worst Page

AN: Thank you to my reviewers, you have no idea how much reviews make my day, my week, and mostly my month. To Sark 79, the first chapter is the only chapter that will be in first person. I thought it might be hard to work in Jason without giving my idea of his background and first person made it really easy to express his emotions. From now on it will be 3rd person, which is how I originally planned it. Thank you, though, for voicing your opinion. Apple, glad you liked it! Agentalana, I agree with you, but once my story is done I would love to read yours and compare. TheUptownGirl, glad you're interested. erak, I'm going to work on my chapters getting longer and longer. The first chapter was short because it was just the prologue. And to charmedgal005, thanks so much for the review and the inspiration. Who knew our conversation would go here? Well, here's chapter 2. Hope you all like it!! (P.S. There's a little bit of language later on. Just thought I ought to warn you!)  
  
Sydney stared disbelievingly at the papers. S.A.B. 47 was typed at the top of each one. Yes, she knew that as a child, she had been trained to be a spy. Her father was scared that her mother would do it, so he did it first. And Sydney had believed him. But these papers showed her what he hadn't told her. That once the project worked on her, Jack passed it on to the rest of the CIA and they began making more training programs. The problem was that once rumors had started circulating that the KGB was using the technology, they needed a new project.  
So Jack made a new project. Or an outline to one, anyway. He told the agency that it would probably be safer to completely brainwash agents. If they didn't feel any obligation to their past, they would do whatever the CIA told them to. They would be injected with a liquid that, when they refused to do or failed missions, would give them headaches. And if they ignored their headaches, they would be killed. Most likely by fellow agents.  
The last paper was the worst. It held information that would sever ties between her and her father for all time. It was the crushing blow.  
_ I, Jack Bristow, being a senior CIA agent and the agent responsible for creating Project: Christmas and Project: Treadstone, give permission for my daughter to be subjected to Treadstone training. Though my daughter may not give her consent, I contend that force be used if necessary. This information will be withheld from all in the Los Angeles branch due to their personal relations with my daughter.  
Once her training for Treadstone is complete, my daughter will no longer know who she was, only that she is an operative. With this in place, I believe we can finally complete what was meant all along. Once Sydney has become someone else, I am sure she will not only become a better operative, I know that she will consent to whatever is necessary to complete the Prophecy. I suggest that plans be made to conceal this project. I have funds, but I cannot be tagged with this. I suggest you find some rogue group, something on the brink of destruction, for us to take. We will work out other plans later.  
Jack Bristow  
_  
Printed on the back of the sheet was the reply.  
_Jack,  
I think I've found our answer. I was running through the intelligence briefing that was recently sent to the Los Angeles office and noticed something. There was one group on there that may fit our needs. They are falling apart at the seams, but they can help us nonetheless. They are followers of Rambaldi who have been studying phrases in his works. They believe that he hid the name of his successor, the one who would put together his works, in one of his documents. I highly doubt that they are right, but it might just hold the right amount of cover for us to begin our work. They believe that a paper they were sent gives them their reason for work. It was a pact between Rambaldi and an unknown source to protect his works until the time came for his successor to rise. Because of this "pact", they are known as The Covenant. They need money, resources, and a reason to continue. But, I believe that once we take over, we can make them one of the most powerful organizations the CIA has ever seen. I even have a few people in mind to pass the organization over to when it gets big because, as it gets going, it will get more coverage by the CIA. As you said, we cannot be tagged with this. But, I believe this will work.  
I will continue my work with Project: Treadstone. We have a new search going on for some new agents. Once Sydney is brainwashed, I'm sure she will be perfect for our team. There is one agent that is excelling greatly who I think she would love to meet. He is David Webb, but we have gotten him to believe his name is Jason Bourne. He's the best I've ever seen. We will be putting him in the field soon. Contact me as soon as you're set.  
Ted Conklin  
_  
Both pages were dated about one month before The Covenant took Sydney. So in that month, Sydney rationalized, her father and Conklin had made The Covenant powerful and set up her capture. Her father pretty much created The Covenant, or at least made it what it was today. He had sacrificed her for the stupid Prophecy! As Sydney reveled on these thoughts, tears began to fall down her face. How could yet another person close to her betray her? When she heard footsteps, Sydney's head shot up.  
"Sydney, you were never supposed to have found this." Jack said with a scowl on his face.  
"How dare you! You come here and tell me I wasn't supposed to find this. You should be apologizing. But, that wouldn't really make a difference with me, because I cannot believe you! When Lauren told me I didn't know who controlled me, I thought she was crazy. But, I guess she was right. You did this to me! You let me get captured! You took away everyone I loved and planned it that I would never remember them again."  
"Sydney, it was only a matter of time until things fell apart. There's always another enemy, always someone willing to take you away. One little thing could happen and you would lose everyone anyway. This was the only way to protect you from that heartbreak."  
"You bastard! Who are you to decide what will happen to me or what will happen to my friends? I found out, didn't I? When I was held. I bet I found out something on you. That's why I'd said I'd seen too much. Had I not lost Vaughn, I would have gone back to him." While she yelled, Sydney slowly slipped her hand into her pocket to grasp her dart gun. "But I had no one. I found out that I couldn't even trust my last bit of family and I couldn't stand it. So instead of telling Kendall, I erased my own memory." Sydney stood, now defiant. "You have ruined my life for the last time, you son of a bitch!"  
"I'm sorry, but I cannot let you go back to L.A. knowing all of this." Jack looked adamant. He began to reach into his breast pocket to grab his gun, but Sydney beat him to the punch. The dart flew to Jack and he crumpled to the ground. Sydney quickly packed all the papers into her briefcase and began to walk out. When she passed her father, she saw that he was still a little awake. Not enough to stop her, but enough to know what she was doing.  
"Guess what, Dad? That dart was pretty high powered. You'll be out for hours, if not days. And by the time you decide to show your face in the U.S. again, I swear to you, the CIA will be looking for you. I'll be in L.A. by the time your body decides to heal. So I guess the next time I see you, you'll probably be in jail. And if not, I will put you there. Night, Dad." Sydney walked out of the room, up the stairs, and out of the bank. Outside, a black van was waiting. She got in and looked up. The two agents that had come with her were now looking right at her, waiting for an order. "Call ahead to the airfield. We need that plane ready to take off the second we get there. I'm calling Dixon right now. Let's go!" The agents nodded and the car sped away. As they sent the call to the airfield, Sydney pulled out her cell and dialed the direct line to Dixon's office.  
"Director Dixon's office."  
"It's Sydney, I need to speak with him right now."  
"I'll put you through." There was a silence for a second and then there was a click.  
"Dixon."  
"It's me. We're headed for the airport right now."  
"Did you find anything in the deposit box?" Sydney sighed.  
"Dixon, I need you to believe what I'm about to say. I found documents on The Covenant. Information about how it became big and why they took me."  
"Sydney, that's great! This is the kind of information we need to destroy them! How long..."  
"There's more. I found out who was responsible for all of it. My kidnapping, my missing years, my erasing my memory, everything! He might even be a Covenant agent right now. I'm not sure. I just know that he came to the back to try to stop me."  
"Who, Syd? Who's the guy?"  
"My father."

AN: I loved writing this chapter, so I hope you enjoyed reading it! Please R&R, it keeps me writing!!


	3. One Last Mission

AN: I am so sorry it took me this long to update. I just started my first year of high school and it has been crazy. But, I could not get this fic off my mind, so here is the next chapter! Oh yeah, the 3's later on are to separate the chapter cause I can't do stars anymore.

LAX was as crowded as it was rumored to be. People were just flying all over thee place. It was funny, though, that security hadn't stopped him. He thought the CIA had all his aliases tagged by now. Apparently, David Webb wasn't tagged. All the better for him.

Jason Bourne walked out to the street and hailed the first taxi he found. Without thinking, he gave the address he had memorized on the plane ride there. It was a Treadstone safe house in the suburbs of Los Angeles. It would hold him while he pursued his leads to this man who had ruined his life.

Once inside the house, he set down his bag and went right to the phone. It was time to work. He dialed the number and waited patiently.

"Hello?"

"It's me. I'm in LA. You said once I was here that you would help me find the man. So, what do you know?"

"I know everything. The operative you're looking for is named Jack Bristow. Unfortunately, he's out of the country right now." Jason was angry.

"He's gone? So you lead me here for nothing?"

"Of course not, Mr. Bourne, I wouldn't do that. What you should do is go to the private airbase off the Santa Monica pier. There will be a plane landing there in 2 hours. A woman named Sydney Bristow will get off the plane, and she will be very upset."

"Wait! How is she related to Jack Bristow?"

"She's his daughter."

"Did he train her too?"

"Yes, and without her permission. She was kidnapped two years ago and forcibly trained. She resisted, though, and even tried to take down the organization. But she found out about her father and she lost it. She underwent surgery and had her memories erased."

"How could a father do that?"

"You don't know Jack Bristow. He's more complicated than he seems. But you should follow my advice. Go to the airfield. When you find her, tell her that you were trained by Projects: Christmas and Treadstone. Ask her to help you."

"With what?"

"Taking down the Covenant. Not only are they trying to get Rambaldi artifacts, they are the ones making funds for training people for Project: Treadstone. Take them down and you will get your revenge."

"What about Jack?"

"I'm taking care of him." He smiled. This could just work out.

"Just one more question. What do you have at stake in this?"

"A lot."

"Please, I want to know who I'm working with."

"What I have at stake is my family. Sydney is my daughter."

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Sydney stepped off the jet exhausted. She had tried to sleep on the plane, but couldn't. Every time she closed her eyes she saw her father standing there. Now, she was headed to the hospital to see Vaughn. After his little stint in Palermo, he needed some medical attention.

"Sydney Bristow?" A voice called into the night. She heard someone run up behind her.

"Whoever you are, I'm sorry but I really don't have time."

"Just listen, please. I was told you were who I needed to contact."

"About what?" She didn't stop walking.

"Project: Christmas and Project: Treadstone." Her feet stopped, but she didn't turn around.

"What about them?"

"I was trained by them. And I want revenge. A source told me that you would help me try to take down the Covenant." Sydney was shocked. Could this be real? It was time to face her mysterious helper. She finally turned and looked at him. When he saw her face, he went into total shock. "Julia?"

_AN: I was going to stop it here, but since it's been so long, I'll give you a double chapter._

"How do you know me?"

"About a year ago, you were on a mission for your employer. They partnered me with you. We broke into a mansion in Beijing to get this scroll. You got the scroll while I carried out my real mission. I was supposed to kill the owner of the mansion. I pegged him in the neck and head and met you back at the car. It was a short relationship, but I remembered you. You had something about you that seemed different."

"I'm sorry I can't say the same..."

"I know you had your memories erased."

"How did you find all of this out?"

"I can't tell you yet. But I can tell you that my source will be meeting us soon. So, are you in?" Sydney looked at both sides. Say no and loose a chance to take down the Covenant. Say yes and probably get in even more trouble with the CIA. She knew the right answer.

"I'm in. Right now, though, I need to go visit someone."

"Sydney, I..."

"Not to turn you in. A friend of mine is in the hospital."

"Oh, okay. I have a house I'm staying in. I'll wait there."

"No, I don't trust anything right now. My father has people everywhere. Here is the address to my house. Wait there for me." She scribbled onto a piece of paper. He took it and began to walk away. "One second, you know my name and I don't know yours."

"Do you want my real name or the name they brainwashed me to believe?"

"Your real name."

"David Webb." She nodded and they both turned in their respective directions. Sydney walked to her car with one thought bouncing around in her head. _'What have I done?' _She shook her head and got in. Once the engine was started, she started barreling down the road to the hospital.

She walked into his room and saw that he was awake.

"Hey." She said slightly above a whisper. He looked at her and a smile came to his face.

"Hi. How was Palermo?"

"Not good." He saw the tears brimming in her eyes and his heart began to break.

"Come here." She willingly went to his side and he wrapped his arms around her. "It's okay, Syd, I'm right here."

"Vaughn, it's my dad. He planned it all. He made another agent training program for the CIA, for adults. I was the test dummy. He took me away from here, from you. He planned it all!" Vaughn felt a searing anger begin to grow in him. About three years ago, the woman he loved had been ripped from his life and it was her father who did it. He made everyone believe that she was dead. _'That son of a bitch.'_

"Sydney, I am so sorry." He stroked her hair as she lay against his shoulder. After she had cried for a while, he lifted her chin so their eyes met. "We can leave, you know, we can get out of this life. All you have to do is say the word and we can be gone." That got a smile out of Sydney.

"Thank you. You have no idea how much that means to me. And I'm starting to think that we should do it." It was Vaughn's turn to smile.

"Really?"

"Yeah. But, there's one last mission we need to do."


	4. Finally

Sydney filled Vaughn in on all that had happened with David. He agreed instantly that this was what they had to do.

"The thing is, Vaughn, we can't let the CIA know about this. The second they hear we're working with someone they were tracking and trying to kill a few months ago, they'll stop us."

"I know. Look, I still have that key your father gave me to his storage facility. We can get most of what we need from there." Sydney smiled.

"Vaughn, that's brilliant." Vaughn was very proud of himself. "When do you get out?"

"Tomorrow morning."

"Okay." Sydney was quiet for a while. Vaughn could see by the look in her eyes, however, that she was making a plan. He took this time to close his eyes and rest a bit.

When they got back from Palermo, he had been brought right to the hospital. Test after test was run and his wound was stitched up again. After that, they had him walk around for a while to make sure no damage had been done. He slept for maybe two hours and then Weiss called him to tell him that Sydney was going to Wittenberg. After that, he couldn't sleep. Whenever Sydney was on missions, even recently, he didn't sleep. So, he spent that time thinking or channel surfing the hospital's 10 channels.

Finally, Sydney looked back up and nodded.

"I'm going to go home and get working with David. You know, set up who we're going to contact and maybe even start planning what to do next. Tomorrow morning, we'll both come pick you up. We'll go to your house so you can pack up and then we'll get on our way. We can't give the CIA any time to contact us or we'll never get away." Vaughn nodded.

"Sounds great."

"Are you sure you're going to be able to do this?"

"Syd, you never have to ask me that. If it has to do with you, I will be able to do anything." Sydney's eyes clouded over as tears threatened to fall. She stood and walked right up to his bed.

"I love you." She said. With that, she leaned down and kissed him. They lingered as long as they could, but finally Sydney and Vaughn broke apart.

"I love you, too." Vaughn's smile was so large that Sydney thought her heart would break. After standing there for a moment more, Sydney turned and walked out.

After a quick drive home, Sydney slipped her key into the front door and walked in. She removed her shoes and coat and then walked to the family room where David was sitting on the couch.

"David?" She called to him, but he didn't turn. "David?" She walked to his side and saw that he was looking at a picture. It had severe fold lines from being opened and refolded multiple times. "Who is she?"

"Marie. She was my girlfriend. When they came after me, she got shot. She's dead." Sydney felt her heart break for him. "She helped me escape the first time, when I didn't know who I was. She protected me. And then she got pegged instead of me."

"I am so sorry, David. I know how it is to lose someone."

"Really? Who'd you lose?"

"My fiancé, Danny. I told him about my working for SD-6 and Arvin Sloane had him killed. I walked in to find him shot and lying in the bathtub."

"Wow, we really do have a lot in common." Sydney gave him an odd look.

"Why does that surprise you?"

"It doesn't. It's just that I was told that we did and now I really know we do."

"Who said we did?"

"Oh, nobody."

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Jack opened his eyes slowly. He was not in the bank in Wittenberg. He was lying on a bed with a very soft pillow under his head. There was a fire in the fireplace in front of him. This was definitely not the bank. He sat up gradually to look around. But he didn't get the chance.

"It's about time. With your resistance to sedatives, I thought you would have been up an hour or two ago." He was very confused at this point. Though he couldn't see the woman's face, he knew her voice. He saw her outline come to him and sit on the bed next to him. "Hello Jack."

"Irina?"

"You knew I'd be back. I've just been biding my time."

"Why did you hide Nadia?"

"Hide her? Jack, I didn't even know her! I wasn't ready to reveal her to the CIA if I hadn't even met her. She was my daughter!"

"You could have told me that. Instead, you just terminated the account and left me asking questions."

"Don't you turn this on me, Jack! I just picked you up off of a vault floor after you pissed off your only daughter." Jack couldn't respond. She was right, of course she was right.

"I'm sorry." Irina was stunned. Jack Bristow barely ever apologized for his actions.

"I'm going to help you. I've sent someone I've discovered to go to Sydney. He knows that I am her mother."

"They're going to take down the Covenant?"

"I know just enough to get them near the top. It's taken quite a bit of favors, but I have the roadmap almost set."

"Favors?" Irina sighed.

"I've used sources from the CIA, former KGB, K-Directorate, on the run Alliance members; anyone I could get my hands on." There was something she wasn't telling him, but Jack couldn't tell what.

"Who else?"

"Before Sydney and Vaughn went missing in North Korea, I had one of my workers contact Sloane for information. Sloane somehow got the guy to confess to working for me. He began contacting me through multiple channels. I didn't respond. He just kept coming. When you told me Sydney was captured, I knew Katya was the one to get the job done. I also knew that if she asked a favor of you, you would do it to save Sydney. So, I told her to have Sloane taken care of. Only at the last minute did I realize that he would be an asset to finding Nadia. That's why Katya told you at the last moment to not do it. But, she called him and told him to back off, albeit against my will. He stopped, though. He went back to obsessing over my daughters." There was a fire in Irina's eyes that gave Jack a quick shiver. Irina saw him shake for a second and smiled. "Don't worry, Jack. By the time I'm done, Sloane will no longer be a problem, the Covenant will be no more, and Sydney will trust you again."

"That sounds almost like a dream."

"It will be real. I promise. And I always keep my promises." Jack tried to hide a yawn, but Irina saw it. "Rest, Jack. When you wake up we'll get back to work." She began to turn away.

"Irina?" She turned back. "Why are you doing this?"

"Because, things need to be made right again. Sloane needs to be jailed for the pain he has caused. The Covenant needs to be stopped for the things they are doing right now. And you need to have your daughter understand you. Once that's done, I can finally stop." Jack was stunned.

"You're going to get out of the intelligence world?"

"Yes. I think I'm going to go back to the CIA. Maybe negotiate a pardon. If Sloane could do it, so can I. I might even move back to Los Angeles." She looked hopeful as she spoke. She had the same hope that Jack was secretly feeling, too. She stood and walked to the door.

"Irina?" She turned one last time. "I missed you."

"I missed you, too. Now, sleep." She left the room and went to her own. Once inside, she fell onto her bed and allowed her hidden tears to reveal themselves. She finally had a chance to make everything right. She was helping her daughter, again. She was taking down Sloane, again. And, she was connecting with her ex-husband, again. Her eyes closed and she let a huge smile set itself on her face. "Finally." Irina whispered into the night.

About an hour later, Irina began to prepare for bed. She changed into sweatpants and a simple top and began to turn down her bed. Then, she heard a knock at the door. She moved softly and opened the door. Jack stood there, looking a bit groggy.

"Jack, what's wrong?"

"I never said thank you." Irina laughed.

"You never need to." Jack cracked a rare smile and looked at Irina as if for the first time. She was so different from when he had last seen her almost two year ago. But, some things hadn't changed, like his feelings for her. Slowly, he leaned down and kissed her. It was gentile and sweet, just like it had been the last time they had been together. "Jack?" Irina whispered.

"Yes?"

"I never told _you _thank you."

"For what?"

"Trusting me again." She wrapped her arms around him and hugged him. "But Jack?"

"Yes?" He laughed at her incessant questions.

"Don't let the CIA know you're working with me again. I couldn't stand to have you locked up for another year."

AN: Ok, so, yeah, sappy. This chapter was kind of a filler, but all this needed to be told now so that I can get on to the REALLY good stuff. If you can't tell, I am a big J/I fan and I miss Spymommy like anything. Next chapter should be up sooner because now that my muse has come out of hiding (Dang thing was eating pizza and laughing at me) and gotten back to work, the ball is finally rolling. Just wait, there's some great stuff coming up!! Please review!


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